Pseudomonas aeruginosa outbreak linked to mineral water bottles in a neonatal intensive care unit: fast typing by use of high-resolution melting analysis of a variable-number tandem-repeat locus

Pseudomonas aeruginosa Detection Using Conventional PCR and Quantitative Real-Time PCR Based on Species-Specific Novel Gene Targets Identified by Pangenome Analysis

Mining novel specific molecular targets and establishing efficient identification methods are significant for detecting Pseudomonas aeruginosa, which can enable P. aeruginosa tracing in food and water. Pangenome analysis was used to analyze the whole genomic sequences of 2017 strains (including 1,000 P. aeruginosa strains and 1,017 other common foodborne pathogen strains) downloaded from gene databases to obtain novel species-specific genes, yielding a total of 11 such genes. Four novel target genes, UCBPP-PA14_00095, UCBPP-PA14_03237, UCBPP-PA14_04976, and UCBPP-PA14_03627, were selected for use, which had 100% coverage in the target strain and were not present in nontarget bacteria. PCR primers (PA1, PA2, PA3, and PA4) and qPCR primers (PA12, PA13, PA14, and PA15) were designed based on these target genes to establish detection methods. For the PCR primer set, the minimum detection limit for DNA was 65.4 fg/μl, which was observed for primer set PA2 of the UCBPP-PA14_03237 gene. The detection limit in pure culture without pre-enrichment was 10⁵ colony-forming units (CFU)/ml for primer set PA1, 10³ CFU/ml for primer set PA2, and 10⁴ CFU/ml for primer set PA3 and primer set PA4. Then, qPCR standard curves were established based on the novel species-specific targets. The standard curves showed perfect linear correlations, with R² values of 0.9901 for primer set PA12, 0.9915 for primer set PA13, 0.9924 for primer set PA14, and 0.9935 for primer set PA15. The minimum detection limit of the real-time PCR (qPCR) assay was 10² CFU/ml for pure cultures of P. aeruginosa. Compared with the endpoint PCR and traditional culture methods, the qPCR assay was more sensitive by one or two orders of magnitude. The feasibility of these methods was satisfactory in terms of sensitivity, specificity, and efficiency after evaluating 29 ready-to-eat vegetable samples and was almost consistent with that of the national standard detection method. The developed assays can be applied for rapid screening and detection of pathogenic P. aeruginosa, providing accurate results to inform effective monitoring measures in order to improve microbiological safety.

Phage Biocontrol of Pseudomonas aeruginosa in Water

Bacteriophage control of harmful or pathogenic bacteria has aroused growing interest, largely due to the rise of antibiotic resistance. The objective of this study was to test phages as potential agents for the biocontrol of an opportunistic pathogen Pseudomonas aeruginosa in water. Two P. aeruginosa bacteriophages (vB_PaeM_V523 and vB_PaeM_V524) were isolated from wastewater and characterized physically and functionally. Genomic and morphological characterization showed that both were myoviruses within the Pbunavirus genus. Both had a similar latent period (50-55 min) and burst size (124-134 PFU/infected cell), whereas there was variation in the host range. In addition to these environmental phages, a commercial Pseudomonas phage, JG003 (DSM 19870), was also used in the biocontrol experiments. The biocontrol potential of the three phages in water was tested separately and together as a cocktail against two P. aeruginosa strains; PAO1 and the environmental strain 17V1507. With PAO1, all phages initially reduced the numbers of the bacterial host, with phage V523 being the most efficient (>2.4 log10 reduction). For the environmental P. aeruginosa strain (17V1507), only the phage JG003 caused a reduction (1.2 log10) compared to the control. The cocktail of three phages showed a slightly higher decrease in the level of the hosts compared to the use of individual phages. Although no synergistic effect was observed in the host reduction with the use of the phage cocktail, the cocktail-treated hosts did not appear to acquire resistance as rapidly as hosts treated with a single phage. The results of this study provide a significant step in the development of bacteriophage preparations for the control of pathogens and harmful microbes in water environments.

The challenge of removing waste from wastewater: let technology use nature!

Tertiary treatments capable of removing chemical and biological contaminants of emerging concern have been successfully developed and implemented at full scale, opening the possibility of using wastewater treatment plants as recycling units, capable of producing wastewater that can be reused in various activities, such as agriculture irrigation; However, tertiary treatments remove only part of the wastewater microbiota, leaving the opportunity for regrowth and/or reactivation of potentially hazardous microorganisms, facilitated by the poor competition among the surviving microorganisms; Under the motto 'added by technology, lead by nature', the treatment and storage of treated wastewater must find the balance to develop a protection shield against the impoverishment the microbial quality and the development of potentially hazardous bacteria.

EasyPrimer: user-friendly tool for pan-PCR/HRM primers design. Development of an HRM protocol on wzi gene for fast Klebsiella pneumoniae typing

In this work we present EasyPrimer, a user-friendly online tool developed to assist pan-PCR and High Resolution Melting (HRM) primer design. The tool finds the most suitable regions for primer design in a gene alignment and returns a clear graphical representation of their positions on the consensus sequence. EasyPrimer is particularly useful in difficult contexts, e.g. on gene alignments of hundreds of sequences and/or on highly variable genes. HRM analysis is an emerging method for fast and cost saving bacterial typing and an HRM scheme of six primer pairs on five Multi-Locus Sequence Type (MLST) genes is already available for Klebsiella pneumoniae. We validated the tool designing a scheme of two HRM primer pairs on the hypervariable gene wzi of Klebsiella pneumoniae and compared the two schemes. The wzi scheme resulted to have a discriminatory power comparable to the HRM MLST scheme, using only one third of primer pairs. Then we successfully used the wzi HRM primer scheme to reconstruct a Klebsiella pneumoniae nosocomial outbreak in few hours. The use of hypervariable genes reduces the number of HRM primer pairs required for bacterial typing allowing to perform cost saving, large-scale surveillance programs.

Multi-drug resistant Pseudomonas aeruginosa and Klebsiella pneumoniae circulation in a burn hospital, Tehran, Iran

Pseudomonas aeruginosa and Klebsiella pneumoniae are among the most important Gram-negative bacteria that can cause nosocomial infections, especially in burn patients. It is important to determine genetic relationships in different clinical specimens as well as between clinical and environmental specimens, which can aid in detecting the source of infection.

The aim of this study was to investigate multi-drug resistant Pseudomonas aeruginosa and Klebsiella pneumoniae spread in a burn hospital, Tehran, Iran. After identification, antibiotic susceptibility testing of all isolates was conducted according to the CLSI guidelines. Further, pulsed-field gel electrophoresis (PFGE) was performed for molecular typing.

97 clinical and 33 environmental specimens were collected. 40 (55%) clinical strains of P. aeruginosa and K. pneumoniae were highly drug resistant. PFGE findings showed similar genetic features to those seen in multi-drug resistant and/or extensively drug resistant P. aeruginosa and K. pneumoniae in clinical and environmental isolates. Inhibition of bacterial spread in the hospital can help to control health care-associated infection and subsequently decrease the morbidity and mortality in hospitalized patients, particularly immunocompromised populations such as burn patients.

ERIC- PCR Typing, RAPD-PCR Fingerprinting and Quorum Sensing Gene Analysis of Pseudomonas aeruginosa Isolated from Different Clinical Sources

Recently, Pseudomonas aeruginosa infections proportions have increased significantly. Molecular typing and virulence analysis are good techniques, which can lead us to know P. aeruginosa infections. P. aeruginosa isolates were identified by using molecular method (16S rDNA gene) via PCR technique for accurate identification. The highest percent 41.26% of P. aeruginosa bacteria was found in the burn infections followed by 28.57% in wound swabs, 17.46% in ear discharge and lowest percentage were obtained from sputum samples. All isolates classified into six groups (A-F) according to classes of antibiotics. Of the 63 bacterial isolates, 100% were resistant to carbencillin, whereas 31.74% were resistant to ticarcillin and all isolates susceptible to imipenem. In addition all of clinical isolates indicated multidrug resistant (MDR) patterns, the highest rate of MDR was observed with pattern C these isolates were able to resist (9-12) antibiotics. All isolates were typed genotypically by using two methods of amplification, ERIC and RAPD-PCR. The results of the ERIC-PCR typing of P. aeruginosa bacteria that 96.82% showed amplification bands ERIC-PCR also revealed 17 groups of genotypes (A-R) and 4 unique isolates. The results of RAPD-PCR fingerprint revealed 12 groups of genotypes (A-M) of 40–90% similarity according to coefficient values and 4 unique isolates, except 7.93% were untypeble. QS genes (lasI, lasR, rhlI, rhlR), screen showed all isolates 100% were positive for one or more QS genes, in the other hand 82.53% carrying lasI, lasR, rhlI, and rhlR, while the 15.87% carrying lasI, rhlI, and rhlR and 1.58% carrying lasI, lasR, and rhlR genes. ERIC genotyping significantly correlated resistance patterns but not with virulence control QS genes. RAPD genotyping significantly correlated with source of infection, resistance patterns and virulence control QS genes. These results can help initial diagnosis MDR P. aeruginosa outbreaks associated with specific genotyping patterns.

Does screening neonates in the neonatal intensive care unit for Pseudomonas aeruginosa colonization help prevent infection?

BACKGROUND

Pseudomonas aeruginosa (PA) is a Gram-negative environmental organism that can cause severe infection in immunosuppressed patients, including preterm neonates. In recent years, it has become common practice to screen neonates for PA colonization.

AIM

To assess the value of screening neonates for PA in (1) predicting the risk of developing severe PA infection and (2) directing infection control practice.

METHODS

Between August 2012 and September 2015, babies admitted to the neonatal intensive care unit (NICU) at North Bristol NHS Trust were screened routinely for PA colonization on admission and weekly thereafter. Data were also collected on babies who developed PA infection. Environmental samples from the NICU were tested for the presence of PA. Variable number tandem repeat (VNTR) typing was performed on all strains of PA from babies and the environment.

FINDINGS

No babies with positive screens subsequently developed PA infection. There was no VNTR strain evidence supporting cross-infection from the environment or other babies.

CONCLUSION

Screening neonates for PA did not identify babies who subsequently developed PA infection. Following cessation of screening in September 2015, there was no increase in the number of babies identified with PA infection.

Review of Antibiotic Resistance in the Indian Ocean Commission: A Human and Animal Health Issue

Antimicrobial resistance (AMR) is a major threat to human, animal health, and environment worldwide. For human, transmission occurred through a variety of routes both in health-care settings and community. In animals, AMR was reported in livestock, pets, and wildlife; transmission of AMR can be zoonotic with the probably most important route being foodborne transmission. The Indian Ocean Commission (IOC), composed of Comoros, Madagascar, Mauritius, Reunion (France), and Seychelles recognized the surveillance of AMR in both animal and human as a main public health priority for the region. Mayotte, French overseas territory, located in Comoros archipelago, was also included in this review. This review summarized our best epidemiological knowledge regarding AMR in Indian Ocean. We documented the prevalence, and phenotypic and genotypic profiles of prone to resistance Gram-positive and Gram-negative bacteria both in animals and humans. Our review clearly pointed out extended-spectrum β-lactamase and carbapenemase-producing Enterobacteriaceae as main human and animal health issue in IOC. However, publications on AMR are scarce, particularly in Comoros, Mayotte, and Seychelles. Thus, research and surveillance priorities were recommended (i) estimating the volume of antimicrobial drugs used in livestock and human medicine in the different territories [mainly third generation cephalosporin (3GC)]; (ii) developing a “One Health” surveillance approach with epidemiological indicators as zoonotic foodborne pathogen (i.e., couple Escherichia coli resistance to 3GC/carbapenems); (iii) screening travelers with a history of hospitalization and consumption of antibiotic drug returning from at risk areas (e.g., mcr-1 transmission with China or hajj pilgrims) allowing an early warning detection of the emergence for quick control measures implementation in IOC.

Sources of sporadic Pseudomonas aeruginosa colonizations/infections in surgical ICUs: Association with contaminated sink trap

BACKGROUND

Many studies have reported the hospital outbreaks of Pseudomonas aeruginosa due to cross-contamination between patients and water fittings, but the importance of water fittings as sources of sporadic P. aeruginosa colonizations/infections remains ambiguous.

AIM

To investigate the sources of sporadic P. aeruginosa colonizations/infections in a clinical intensive surveillance, and further analysis the potential of sink trap for P. aeruginosa transmission in intensive care units (ICUs).

METHODS

Patients monitoring and targeted environmental screening for P. aeruginosa was performed prospectively over a 27-week period, in absence of recognized outbreak, in two surgical intensive care units (SICUs). All isolates were genotyped by Pulsed field gel electrophoresis analysis.

FINDINGS

18.9% (46/244) of water fitting samples harbored P. aeruginosa, and active screening samples from 9.2% (55/595) of hospitalized patients carried with P. aeruginosa. According to genotype results, approximately 50% of P. areuginosa colonizations/infections of patients were of exogenous origin. 64.7% (11/17) of exogenous sourced cases were associated with contaminated sink traps. There was a significant correlation between the incidence of exogenous colonization/infection and the prevalence of P. areuginosa in water fitting in SICU-2 (rs = 0.972; p = 0.014). Furthermore, P. areuginosa from sink trap possessed a higher level of resistance to multi-antibiotics as opposed to cross-transmission from other patients.

CONCLUSION

Water fitting especially sink trap act as an important role in sporadic P. aeruginosa transmission in SICU patients. This report highlights the necessity of identification of potential environmental reservoirs, such as sinks, for control of infections of environmentally hardy multi-resistant P. areuginosa.

Advantages and limitations of potential methods for the analysis of bacteria in milk: a review

Contamination concerns in the dairy industry are motivated by outbreaks of disease in humans and the inability of thermal processes to eliminate bacteria completely in processed products. HACCP principles are an important tool used in the food industry to identify and control potential food safety hazards in order to meet customer demands and regulatory requirements. Milk testing is of importance to the milk industry regarding quality assurance and monitoring of processed products by researchers, manufacturers and regulatory agencies. Due to the availability of numerous methods used for analysing the microbial quality of milk in literature and differences in priorities of stakeholders, it is sometimes confusing to choose an appropriate method for a particular analysis. The objective of this paper is to review the advantages and disadvantages of selected techniques that can be used in the analysis of bacteria in milk. SSC, HRMA, REP, and RAPD are the top four techniques which are quick and cost-effective and possess adequate discriminatory power for the detection and profiling of bacteria. The following conclusions were arrived at during this review: HRMA, REP and RFLP are the techniques with the most reproducible results, and the techniques with the most discriminatory power are AFLP, PFGE and Raman Spectroscopy.

Nosocomial outbreak of Pseudomonas aeruginosa associated with a drinking water fountain

Over a four-month period, ten patients were suspected of having acquired nosocomial infection to P. aeruginosa in the ear, nose, and throat department. Environmental and clinical isolates were compared. Only water from a drinking water fountain was contaminated by P. aeruginosa. This isolate and those of three patients had indistinguishable random amplified polymorphic DNA profiles. These patients had serious oncology diseases. The drinking water fountain was used for their alimentation by percutaneous endoscopic gastrostomy and was the origin of the outbreak. Another type of drinking fountain with a terminal ultraviolet treatment was installed, following which no new infections linked to drinking water were identified.

Use of a New High Resolution Melting Method for Genotyping Pathogenic Leptospira spp

BACKGROUND

Leptospirosis is a worldwide zoonosis that is endemic in tropical areas, such as Reunion Island. The species Leptospira interrogans is the primary agent in human infections, but other pathogenic species, such as L. kirschner and L. borgpetersenii, are also associated with human leptospirosis.

METHODS AND FINDINGS

In this study, a melting curve analysis of the products that were amplified with the primer pairs lfb1 F/R and G1/G2 facilitated an accurate species classification of Leptospira reference strains. Next, we combined an unsupervised high resolution melting (HRM) method with a new statistical approach using primers to amplify a two variable-number tandem-repeat (VNTR) for typing at the subspecies level. The HRM analysis, which was performed with ScreenClust Software, enabled the identification of genotypes at the serovar level with high resolution power (Hunter-Gaston index 0.984). This method was also applied to Leptospira DNA from blood samples that were obtained from Reunion Island after 1998. We were able to identify a unique genotype that is identical to that of the L. interrogans serovars Copenhageni and Icterohaemorrhagiae, suggesting that this genotype is the major cause of leptospirosis on Reunion Island.

CONCLUSIONS

Our simple, rapid, and robust genotyping method enables the identification of Leptospira strains at the species and subspecies levels and supports the direct genotyping of Leptospira in biological samples without requiring cultures.

[Update on outbreaks reported from neonatal intensive care units: Serratia marcescens, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa]

In terms of the unique risk profile, the clinical course of nosocomial infections, and the most prevalent bacterial pathogens, literature on outbreaks of potentially pathogenic bacteria on neonatal intensive care units (NICUs) needs to be analyzed separately from reports derived from other intensive care units. With the purpose of updating important information for those involved in outbreak management and fostering preventive efforts, this article summarizes the results of a systematic literature analysis, referring to an earlier publication by Gastmeier et al. This review focuses on NICU outbreaks caused by Serratia marcescens, Klebsiella pneumoniae, Acinetobacter baumannii, and Pseudomonas aeruginosa.

Aetiology, source and prevention of waterborne healthcare-associated infections: a review

The purpose of this review is to discuss the scientific literature on waterborne healthcare-associated infections (HCAIs) published from 1990 to 2012. The review focuses on aquatic bacteria and describes both outbreaks and single cases in relation to patient characteristics, the settings and contaminated sources. An overview of diagnostic methods and environmental investigations is summarized in order to provide guidance for future case investigations. Lastly, on the basis of the prevention and control measures adopted, information and recommendations are given. A total of 125 reports were included, 41 describing hospitalized children. All cases were sustained by opportunistic pathogens, mainly Legionellaceae, Pseudomonadaceae and Burkholderiaceae. Hot-water distribution systems were the primary source of legionnaires’ disease, bottled water was mainly colonized by Pseudomonaceae, and Burkholderiaceae were the leading cause of distilled and sterile water contamination. The intensive care unit was the most frequently involved setting, but patient characteristics were the main risk factor, independent of the ward. As it is difficult to avoid water contamination by microbes and disinfection treatments may be insufficient to control the risk of infection, a proactive preventive plan should be put in place. Nursing staff should pay special attention to children and immunosuppressed patients in terms of tap-water exposure and also their personal hygiene, and should regularly use sterile water for rinsing/cleaning devices.

Four genotyping schemes for phylogenetic analysis of Pseudomonas aeruginosa: comparison of their congruence with multi-locus sequence typing

Several molecular typing schemes have been proposed to differentiate among isolates and clonal groups, and hence establish epidemiological or phylogenetic links. It has been widely accepted that multi-locus sequence typing (MLST) is the gold standard for phylogenetic typing/long-term epidemiological surveillance, but other recently described methods may be easier to carry out, especially in settings with limited access to DNA sequencing. Comparing the performance of such techniques to MLST is therefore of relevance. A study was therefore carried out with a collection of P. aeruginosa strains (n = 133) typed by four typing schemes: MLST, multiple-locus variable number tandem repeat analysis (MLVA), pulsed-field gel electrophoresis (PFGE) and the commercial DiversiLab microbial typing system (DL). The aim of this study was to compare the results of each typing method with MLST. The Simpson's indices of diversity were 0.989, 0.980, 0.961 and 0.906 respectively for PFGE, MLVA, DL and MLST. The congruence between techniques was measured by the adjusted Wallace index (W): this coefficient indicates the probability that a pair of isolates which is assigned to the same type by one typing method is also typed as identical by the other. In this context, the congruence between techniques was recorded as follow: MLVA-type to predict MLST-type (93%), PFGE to MLST (92%), DL to MLST (64.2%), PFGE to MLVA (63.5%) and PFGE to DL (61.7%). Conversely, for all above combinations, prediction was very poor. The congruence was increased at the clonal complex (CC) level. MLST is regarded the gold standard for phylogenetic classification of bacteria, but is rather laborious to carry out in many settings. Our data suggest that MLVA can predict the MLST-type with high accuracy, and even higher when studying the clonal complex level. Of the studied three techniques MLVA was therefore the best surrogate method to predict MLST.

An integrated approach to control a prolonged outbreak of multidrug-resistant Pseudomonas aeruginosa in an intensive care unit

In this paper we aim to provide insight into the complexity of outbreak management in an intensive care unit (ICU) setting. In October 2010 four patients on the ICU of our tertiary care centre were colonized or infected with a multidrug-resistant strain of Pseudomonas aeruginosa (MDR-PA). An outbreak investigation was carried out and infection control measures were taken in an attempt to identify a potential source and stop transmission. The outbreak investigation included descriptive epidemiology, comprising retrospective case finding by reviewing the laboratory information system back to 2004 and prospective case finding by patient screening for MDR-PA. Furthermore, microbiological analysis, environmental screening and a case-control study were carried out. Infection control measures consisted of re-education of healthcare personnel on basic hygiene measures, auditing of hygiene procedures used in daily practice by infection control practitioners, and stepwise up-regulation of isolation measures. From February 2009 to January 2012, 44 patients on our ICU were found to be MDR-PA positive. MDR-PA isolates of the 44 patients showed two distinct AFLP patterns, with homology within each of the AFLP clusters of more than 93%. The VIM metallo-β-lactamase gene was detected in 20 of 21 tested isolates. A descriptive epidemiology investigation identified the rooms with the highest numbers of MDR-PA positive patients. The case-control study showed three factors to be independently associated with MDR-PA positivity: admission to ICU subunit 1 (OR, 6.1; 95% CI, 1.7, 22), surgery prior to or during admission (OR, 5.7; 95% CI, 1.6, 20) and being warmed-up with the warm-air blanket (OR, 3.6; 95% CI, 1.2, 11). After three environmental screening rounds, with sampling of sinks, furniture and devices in the ICU, without revealing a clear common source, a fourth environmental investigation included culturing of faucet aerators. Two faucets were found to be positive for MDR-PA and were replaced. The occurrence of new cases decreased with the strengthening of infection control measures and declined further with the removal of the common source. With this integrated approach a prolonged outbreak of P. aeruginosa was controlled. Contaminated faucet aerators on the ICU probably served as a persisting source, while interpatient transmission by medical staff was a likely way of spread. Seven months after the last case (January 2012) and 3 months after cessation of extended isolation measures (May 2012), single cases started to occur on the ICU, with a total of seven patients in the past year. No common source has yet been found.

Genotyping of present-day and historical Geobacillus species isolates from milk powders by high-resolution melt analysis of multiple variable-number tandem-repeat loci

Spores of thermophilic Geobacillus species are a common contaminant of milk powder worldwide due to their ability to form biofilms within processing plants. Genotyping methods can provide information regarding the source and monitoring of contamination. A new genotyping method was developed based on multilocus variable-number tandem-repeat (VNTR) analysis (MLVA) in conjunction with high-resolution melt analysis (MLV-HRMA) and compared to the currently used method, randomized amplified polymorphic DNA PCR (RAPD-PCR). Four VNTR loci were identified and used to genotype 46 Geobacillus isolates obtained from retailed powder and samples from 2 different milk powder processing plants. These 46 isolates were differentiated into 16 different groups using MLV-HRMA (D = 0.89). In contrast, only 13 RAPD-PCR genotypes were identified among the 46 isolates (D = 0.79). This new method was then used to analyze 35 isolates obtained from powders with high spore counts (>10(4) spores · g(-1)) from a single processing plant together with 27 historical isolates obtained from powder samples processed in the same region of Australia 17 years ago. Results showed that three genotypes can coexist in a single processing run, while the same genotypes observed 17 years ago are present today. While certain genotypes could be responsible for powders with high spore counts, there was no correlation to specific genotypes being present in powder plants and retailed samples. In conclusion, the MLV-HRMA method is useful for genotyping Geobacillus spp. to provide insight into the prevalence and persistence of certain genotypes within milk powder processing plants.

Novel strategy to evaluate infectious salmon anemia virus variants by high resolution melting

Genetic variability is a key problem in the prevention and therapy of RNA-based virus infections. Infectious Salmon Anemia virus (ISAv) is an RNA virus which aggressively attacks salmon producing farms worldwide and in particular in Chile. Just as with most of the Orthomyxovirus, ISAv displays high variability in its genome which is reflected by a wider infection potential, thus hampering management and prevention of the disease. Although a number of widely validated detection procedures exist, in this case there is a need of a more complex approach to the characterization of virus variability. We have adapted a procedure of High Resolution Melting (HRM) as a fine-tuning technique to fully differentiate viral variants detected in Chile and projected to other infective variants reported elsewhere. Out of the eight viral coding segments, the technique was adapted using natural Chilean variants for two of them, namely segments 5 and 6, recognized as virulence-associated factors. Our work demonstrates the versatility of the technique as well as its superior resolution capacity compared with standard techniques currently in use as key diagnostic tools.

A novel method for simultaneous Enterococcus species identification/typing and van genotyping by high resolution melt analysis

In order to develop a typing and identification method for van gene containing Enterococcus faecium, two multiplex PCR reactions were developed for use in HRM-PCR (High Resolution Melt-PCR): (i) vanA, vanB, vanC, vanC23 to detect van genes from different Enterococcus species; (ii) ISR (intergenic spacer region between the 16S and 23S rRNA genes) to detect all Enterococcus species and obtain species and isolate specific HRM curves. To test and validate the method three groups of isolates were tested: (i) 1672 Enterococcus species isolates from January 2009 to December 2009; (ii) 71 isolates previously identified and typed by PFGE (pulsed-field gel electrophoresis) and MLST (multi-locus sequence typing); and (iii) 18 of the isolates from (i) for which ISR sequencing was done. As well as successfully identifying 2 common genotypes by HRM from the Austin Hospital clinical isolates, this study analysed the sequences of all the vanB genes deposited in GenBank and developed a numerical classification scheme for the standardised naming of these vanB genotypes. The identification of Enterococcus faecalis from E. faecium was reliable and stable using ISR PCR. The typing of E. faecium by ISR PCR: (i) detected two variable peaks corresponding to different copy numbers of insertion sequences I and II corresponding to peak I and II respectively; (ii) produced 7 melt profiles for E. faecium with variable copy numbers of sequences I and II; (iii) demonstrated stability and instability of peak heights with equal frequency within the patient sample (36.4±4.5 days and 38.6±5.8 days respectively for 192 patients); (iv) detected ISR-HRM types with as much discrimination as PFGE and more than MLST; and (v) detected ISR-HRM types that differentiated some isolates that were identical by PFGE and MLST. In conjunction with the rapid and accurate van genotyping method described here, this ISR-HRM typing and identification method can be used as a stable identification and typing method with predictable instability based on recombination and concerted evolution of the rrn operon that will complement existing typing methods.

Rapid and sensitive detection of Pseudomonas aeruginosa in chlorinated water and aerosols targeting gyrB gene using real-time PCR

AIMS

For the rapid detection of Pseudomonas aeruginosa from chlorinated water and aerosols, gyrB gene-based real-time PCR assay was developed and investigated.

METHODS AND RESULTS

Two novel primer sets (pa722F/746MGB/899R and pa722F/746MGB/788R) were designed using the most updated 611 Pseudomonas and 748 other bacterial gyrB genes for achieving high specificity. Their specificity showed 100% accuracy when tested with various strains including clinical isolates from cystic fibrosis patients. The assay was tested with Ps. aeruginosa-containing chlorinated water and aerosols to simulate the waterborne and airborne transmission routes (detection limit 3·3 × 10² CFU per PCR-2·3 × 10³ CFU per PCR). No chlorine interference in real-time PCR was observed at drinking water level (c. 1 mg l⁻¹), but high level of chorine (12 mg l⁻¹) interfered the assay, and thus neutralization was needed. Pseudomonas aeruginosa in aerosol was successfully detected after capturing with gelatin filters with minimum 2 min of sampling time when the initial concentration of 10⁴ CFU ml⁻¹ bacteria existed in the nebulizer.

CONCLUSIONS

A highly specific and rapid assay (2-3 h) was developed by targeting gyrB gene for the detection of Ps. aeruginosa in chlorinated water and aerosols, combined with optimized sample collection methods and sample processing, so the direct DNA extraction from either water or aerosol was possible while achieving the desired sensitivity of the method.

SIGNIFICANCE AND IMPACT OF THE STUDY

  The new assay can provide timely and accurate risk assessment to prevent Ps. aeruginosa exposure from water and aerosol, resulting in reduced disease burden, especially among immune-compromised and susceptible individuals. This approach can be easily utilized as a platform technology for the detection of other types of micro-organisms, especially for those that are transmitted via water and aerosol routes, such as Legionella pneumophila.

Rapid genotyping of Achromobacter xylosoxidans, Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa and Stenotrophomonas maltophilia isolates using melting curve analysis of RAPD-generated DNA fragments (McRAPD)

Typing of bacteria is important for monitoring newly emerging pathogens and for examining local outbreaks. We evaluated the randomly amplified polymorphic DNA technique in combination with melting curve analysis (McRAPD) of the amplified DNA fragments to genotype isolates from five Gram-negative species, i.e. Achromobacter xylosoxidans, Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa and Stenotrophomonas maltophilia. By determining the melting temperature peaks of the amplified DNA fragments, we were able to distinguish the different genotypes of isolates, as they had been assessed by other genotyping techniques, i.e. agarose gel electrophoresis of RAPD fragments, multilocus sequence typing and/or AFLP™. According to our results, McRAPD may offer the possibility of genotyping a limited number of bacterial isolates, e.g. in case of suspicion of hospital outbreak, via a less costly, more rapid, less laborious and more user-friendly technique than RAPD followed by electrophoresis.